The first thing to note is that Chief Justice Roberts and the other justices who wrote opinions were kinder to the Obama administration than it deserved. The administration came out entirely against the concept of the ministerial exception to anti-discrimination statutes, a legal principle that has been commonplace in the courts of appeals for nearly four decades. The Obama Department of Justice, representing the EEOC, took the position that some protection might be afforded to religious organizations on freedom of association grounds, which are only implicit in the First Amendment, but rejected any recourse to what the text of the amendment says about religious freedom. This, the chief justice mildly said, was untenable.

One question now is whether Hosanna-Tabor can be squared with the 1990 Employment Division v. Smith decision, in which the Court held that the First Amendment does not mandate that religious exceptions be made to generally applicable laws. The chief justice said that the Americans With Disabilities Act, at issue here, like Oregons prohibition on peyote use [at issue in Smith ], is a valid and neutral law of general applicability. He went on:

But a churchs selection of its ministers is unlike an individuals ingestion of peyote. Smith involved government regulation of only outward physical acts. The present case, in contrast, concerns government interference with an internal church decision that affects the faith and mission of the church itself . . . . The contention that Smith forecloses recognition of a ministerial exception rooted in the Religion Clauses has no merit.

What Roberts suggests here is an important qualification of Smith . Quoting a nineteenth century ruling, Justice Scalia (who silently joined yesterdays ruling) said in Smith that a blanket rule that religious claims nearly always trigger exemptions to generally applicable laws would in effect permit every citizen to become a law unto himself. Yesterday, in Hosanna-Tabor , Chief Justice Roberts said, in effect, that when it comes to the right to govern themselves in the choice of their clergy, ministers, leaders, and others whose functions and duties are distinctly religious, churches and other religious organizations are indeed a law unto themselves. This is an important recognition of the communal nature of religious life, but it does leave Smith largely intact in the context that gave rise to it two decades ago.

There may be a straw in the wind in yesterdays ruling, with respect to the Obama administrations determination to compel the coverage of contraceptive and abortifacient drugs in health insurance policies, even ones for religious institutions. The only religious exception offered so far by the Department of Health and Human Services to its contraceptive coverage mandate is an exemption so narrow, for religious organizations that employ and serve only their own co-religionists, that even the ministry of Jesus would not qualify. It is as though the Obama administration is staffed by people who have never encountered the ministry to the world that is so common among religious folk”especially but not uniquely among Christians.

A similar mistake was made by the Sixth Circuit, whose decision against the school was reversed by the Supreme Court. Cheryl Perich, whose complaint against the school under the ADA gave rise to the case, was a called teacher who was considered by the school, and considered herself, to be a commissioned minister of the Lutheran church. But as a teacher of secular subjects, she spent only a minority of her time at Hosanna-Tabor in overtly religious activities. This caused the Sixth Circuit to conclude that she was not really a minister for purposes of the ministerial exception. Roberts set the record straight:

It is true that her religious duties consumed only 45 minutes of each workday, and that the rest of her day was devoted to teaching secular subjects. The EEOC regards that as conclusive, contending that any ministerial exception should be limited to those employees who perform exclusively religious function. . . . We cannot accept that view. Indeed, we are unsure whether any such employees exist. The heads of congregations themselves often have a mix of duties, including secular ones, such as helping to manage the congregations finances, supervising purely secular personnel, and overseeing the upkeep of facilities.

Likewise, a Catholic hospital, or a Christian college, or church, synagogue, or mosque running a soup kitchen is chiefly engaged in activities that might be called secular: healing, teaching, feeding the poor. But they do these things in response to a calling to serve the world, a calling that flows out of a wellspring of faith. They must not be asked, in order to pursue that calling, to betray their faith by acceding to insurance rules they regard as immoral.

Justice Alito, in a concurring opinion joined by Justice Kagan, wrote that we have long recognized that the Religion Clauses protect a private sphere within which religious bodies are free to govern themselves in accordance with their own beliefs. Courts, he wrote, must avoid inquiring into whether religious reasons given for internal governance decisions are merely pretexts for evading legal obligations. In order to probe the real reason . . . a civil court”and perhaps a jury”would be required to make a judgment about church doctrine. Just imagine a civil factfinder sitting in ultimate judgment of what the accused church really believes, and how important that belief is to the churchs overall mission.

This is just what the Obama HHS is trying to do with its insurance mandate”make a political judgment that the beliefs of Catholics and others regarding contraception and abortion are not really important to the overall mission of religious hospitals, schools, and soup kitchens” as the government understands that mission . This struggle looks more like Hosanna-Tabor than like Smith . The Obama administration deserves to be rebuked for the hostility to religious liberty in its proposed HHS rules, for the same reasons its EEOC lost yesterday.

Matthew J. Franck is Director of the William E. and Carol G. Simon Center on Religion and the Constitution at the Witherspoon Institute in Princeton, New Jersey.